Protein target profile

KP13_00058

D-galactonate dehydratase

Genome: KpKP13 Gene: dgoD AHE41982.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3H0G1
Length 382
Pocket druggability 0.604
Direct ligand evidence 0 57 total records
Functional annotation 1 EC 4 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
Hit
Human identity (%)
25.773 Lower values reduce human off-target concern.
Human E-value
4.31e-10
Gut microbiome similarity
4.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
94.92 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.604
Structure A0A0H3H0G1
Pocket Pocket 1
P2Rank 0.936
Structure A0A0H3H0G1
Pocket Pocket 1
ColabFold model
FPocket 0.388 · Pocket 11
P2Rank 0.924 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 196 / 4744 genomes with a hit
Prevalence 4.1%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

Primary amino-acid sequence viewer.

MKITNITTYRLPPRWMFLKIETDEGIVGWGEPVIEGRARTVEAAVHEFGDYLIGQDPARINDLWQVMYRGGFYRGGPIMMSAIAGIDQALWDIKGKVLNAPVWQLMGGLVRDKIKAYSWVGGDRPAEVIDGIKKLRGIGFDTFKLNGCEEMGIIDNSRAVDAAVNTVAQIREAFGNEIEFGLDFHGRVSAPMAKVLIKELEPYRPLFIEEPVLAEQAEYYPRLAAQTHIPIAAGERMFSRFEFKRVLEAGGVAILQPDLSHAGGITECYKIAGMAEAYDVGLAPHCPLGPIALAACLHVDFVSHNAVFQEQSMGIHYNKGAELLDFVKNKEDFNMEGGFFKPLMKPGLGVEIDEARVIELSKNAPDWRNPLWRYEDGSVAEW

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0008869 Catalysis of the reaction: D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O.
  • GO:0034194 The chemical reactions and pathways resulting in the breakdown of D-galactonate, the anion of D-galactonic acid.
  • GO:0009063 The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents.
  • GO:0000287 Binding to a magnesium (Mg) ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

29 records
Show feature table
Start End DB Term Name
107 342 FunFam G3DSA:3.20.20.120:FF:000008 D-galactonate dehydratase
102 345 Gene3D G3DSA:3.20.20.120 -
102 345 InterPro IPR036849 Enolase-like, C-terminal domain superfamily
125 230 SMART SM00922 MR_MLE_2
125 230 InterPro IPR013342 Mandelate racemase/muconate lactonizing enzyme, C-terminal
15 107 Pfam PF02746 Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
15 107 InterPro IPR013341 Mandelate racemase/muconate lactonizing enzyme, N-terminal domain
139 355 Pfam PF13378 Enolase C-terminal domain-like
139 355 InterPro IPR029065 Enolase C-terminal domain-like
2 353 CDD cd03325 D-galactonate_dehydratase
2 353 InterPro IPR023592 D-galactonate dehydratase
180 211 ProSitePatterns PS00909 Mandelate racemase / muconate lactonizing enzyme family signature 2.
180 211 InterPro IPR018110 Mandelate racemase/muconate lactonizing enzyme, conserved site
1 369 SFLD SFLDF00003 D-galactonate dehydratase
1 369 InterPro IPR023592 D-galactonate dehydratase
1 362 PANTHER PTHR48080 D-GALACTONATE DEHYDRATASE-RELATED
1 362 InterPro IPR034593 D-galactonate dehydratase DgoD-like
95 357 SUPERFAMILY SSF51604 Enolase C-terminal domain-like
95 357 InterPro IPR036849 Enolase-like, C-terminal domain superfamily
14 357 Gene3D G3DSA:3.30.390.10 -
14 357 InterPro IPR029017 Enolase-like, N-terminal
1 112 SUPERFAMILY SSF54826 Enolase N-terminal domain-like
1 112 InterPro IPR029017 Enolase-like, N-terminal
82 107 ProSitePatterns PS00908 Mandelate racemase / muconate lactonizing enzyme family signature 1.
82 107 InterPro IPR018110 Mandelate racemase/muconate lactonizing enzyme, conserved site
1 116 FunFam G3DSA:3.30.390.10:FF:000003 D-galactonate dehydratase
1 369 SFLD SFLDS00001 Enolase
1 382 Hamap MF_01289 D-galactonate dehydratase [dgoD].
1 382 InterPro IPR023592 D-galactonate dehydratase

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #1
0.604
Likely same site as P2Rank 1 3.5 Å 17 shared residues 94% of smaller site
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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.936
Likely same site as FPocket 1 3.5 Å 17 shared residues 94% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.025
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Surrounding area
Site 3 P2Rank #3
0.006
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Surrounding area
Residue sets
UniProt: Active site:185-185 Proton donor/acceptor
UniProt: Active site:285-285 Proton donor/acceptor
UniProt: Binding site:183-183
UniProt: Binding site:209-209
UniProt: Binding site:235-235
UniProt: Site:258-258 Increases basicity of active site His
UniProt: Site:310-310 Transition state stabilizer
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3H0G1
AlphaFold DB full sequence Viewing
ColabFold KP13_00058
ColabFold full sequence Loaded

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

57 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 7 records from similar proteins
Structural ligands 7 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
CS2 PDB via homolog 196.2 Da · LogP -3.49 · TPSA 138.5 Open detail RCSB PDB
EZ4 PDB via homolog Detail RCSB PDB
KDG PDB via homolog Detail RCSB PDB
LMR PDB via homolog Detail RCSB PDB
MLT PDB via homolog Detail RCSB PDB

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
CS2 RCSB PDB Q1QT89 196.2 Da LogP -3.49 TPSA 138.5 1 viol. ✓ Clean C([C@H]([C@H]([C@@H]([C@@H](C(=O)O)O)O)O)O)O
EZ4 RCSB PDB Q1QT89 179.1 Da LogP -2.65 TPSA 127.4 ✓ Ro5 ✓ Clean C([C@H]([C@H]([C@@H](C(=O)N=O)O)O)O)O
KDG RCSB PDB Q1QT89 178.1 Da LogP -2.26 TPSA 115.1 ✓ Ro5 ✓ Clean C([C@@H]([C@@H](CO)O)O)C(=O)C(=O)O
LMR RCSB PDB B9JNP7 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)O)C(=O)O
MLT RCSB PDB B2UCA8 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)C(=O)O
NHE RCSB PDB B3PDB1 207.3 Da LogP 0.80 TPSA 66.4 ✓ Ro5 ✓ Clean C1CCC(CC1)NCCS(=O)(=O)O
TLA RCSB PDB B3PDB1 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=O)O)O

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.